Enhanced reaction performance is what has piqued interest in using graphene-based catalysts in producing biodiesel. However, in-depth analyses were lacking from a kinetic and thermodynamic standpoint. This means that a well-designed experiment is necessary to determine the effect that the graphene catalysts have on the reaction rates and yields. This work addresses the kinetic and thermodynamic aspects of heterogeneously catalyzed transesterification using sulphonated biomass-derived graphene catalysts, i.e., bGO-SO3H and brGO-SO3H. It was accomplished using the pseudo-first order mechanism and the Eyring-Polanyi equation, with all data fitting satisfactorily in both models at the ideal reaction temperature of 353.15 K, resulting in R2 values of 0.9784 (bGO-SO3H) and 0.9884 (brGO-SO3H). The calculated activation energy (Ea) was determined to be 44.45 and 51.73 kJ mol-1 for bGO- and brGO-SO3H, respectively. Additionally, the Gibbs free energy (ΔG) values were determined at −38.09 and −31.81 kJ mol−1 for bGO- and brGO-SO3H, respectively. Meanwhile, the values for ΔH and ΔS were obtained as 41.69 kJ mol−1 and 225.93 J mol−1 K−1, respectively, and 48.96 kJ mol−1 and 228.72 J mol−1 K−1, respectively. These collective outcomes collectively signify the endothermic nature of the reaction and their spontaneity, particularly under elevated temperature conditions.